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You play professor Alan Russell, an eco-activist who was offered by a company named Subtech to design Biosphere 4. Biospheres are large complexes holding artificial ecosystems. Russell wanted to develop a synthetic plant that could efficiently transform CO2 into oxygen. But those plants soon turn to be killers: they can move and suck CO2 from the lungs of human beings. Russell opposes any further works connected to those plants, but Subtech continues the researches and is unable to prevent a disaster...

Russell is trapped in Biosphere 4 and has to find his way out. There are four ecosystems ("biomes") in Biosphere 4: rainforest, savannah, ocean, and accelerated evolution. Russell has to overcome all obstacles and to stay alive in this bizarre world.

Biosys is an adventure game with simulation elements. You control the environment in the artificial world, but you also have to take care of your own condition. You must drink, eat, and sleep. Different kinds of nutrition will have different effects upon you, your condition will change depending on where you decided to sleep, etc. The rest is standard puzzle-solving gameplay: finding items, operating switches, etc.